As a method of measuring homocysteine, a method of reacting homocysteine in a sample with homocysteine methyltransferase and D-methionine methylsulfonium, and then detecting the produced D-methionine with D-amino acid oxidase has been reported (see WO 02/02802). However, it is known that biological samples contain D-amino acids such as D-alanine and D-serine in small amounts, and these amino acids increase in the case of renal diseases or the like (e.g., see Fukushima, T., Biol. Pharm. Bull., 1995, Vol. 18, No. 8, pp. 1130–1132). It is believed that D-alanine and D-serine, which can be a substrate of D-amino acid oxidase, leads to a positive reading in the method of measuring homocysteine. Therefore, as described in WO 02/02802, in order to avoid the influence of endogenous D-amino acids that are originally present in a sample, it is necessary to subtract a value obtained by measurement by the same operation except that homocysteine methyltransferase is not contained from a measured value in the case of containing this enzyme. That is to say, it is necessary to provide a sample blank for each individual sample to measure the amount of endogenous D-amino acids.